MIQL 2.7

The Molecular Interactions Query Language (MIQL) defines a way to allow more powerful and flexible queries by using a specific syntax when doing searches. If we have a common way to access the data (PSICQUIC), we need a common way to write the search queries.
In most cases, searches are done for a specific identifier or group of identifiers. However, the service is not limited to these. For instance, there are ways to search for specific organisms, interaction detection methods or publication identifiers. The MIQL defines how these kind of queries can be done.

MIQL is a consensus between the different databases, so you should be able to use the same query across different repositories. It is based on the PSIMITAB 2.7 format and allows to search for data in specific columns, by using the fields explained in the next section.

The MIQL syntax is based on Lucene's syntax. A query is broken into terms and operators:

Terms: single words or phrases (group of words surrounded by quotes). E.g. brca2 or "pull down"

Fields: used to search in a specific column. See the next section for the specific field names. E.g. species:human

IMPORTANT: When using parenthesis in your queries, please add a space after and opening parenthesis and before a closing one, since some PSICQUIC implementations need it for correct parenthesis recognition.

Fields

The following table shows the available standard fields that can be used in PSICQUIC searches:

Field Name

Searches on

MITAB 2.7 Columns

Example

idA

Identifier A

1

idA:P74565

idB

Identifier B

2

idB:P74565

id

Identifiers (A or B)

1..4

id:P74565

alias

Aliases (A or B)

5, 6

alias:( KHDRBS1 OR HCK )

identifier

Identifiers (A or B) or Alternatives (A or B) Aliases (A or B)

1..6

identifier:P74565

pubauth

Publication 1st author(s)

8

pubauth:scott

pubid

Publication Identifier(s)

9

pubid:( 10837477 OR 12029088 )

taxidA

Tax ID interactor A: be it the tax ID or the species name

10

taxidA:mouse

taxidB

Tax ID interactor B: be it the tax ID or species name

11

taxidB:9606

species

Species. Tax ID A and Tax ID B

10, 11

species:human

type

Interaction type(s)

12

type:"physical association"

detmethod

Interaction Detection method(s)

7

detmethod:"two hybrid*"

interaction_id

Interaction identifier(s)

14

interaction_id:EBI-761050

pbioroleA

Biological role A

17

pbioroleA:ancillary

pbioroleB

Biological role B

18

pbioroleB:"MI:0684"

pbiorole

Biological roles (A or B)

17, 18

pbiorole:enzyme

ptypeA

Interactor type A

21

ptypeA:protein

ptypeB

Interactor type B

22

ptypeB:"gene"

ptype

Interactor types (A or B)

21, 22

pbiorole:"small molecule"

pxrefA

Interactor xref A (or Identifier A)

23, 1

pxrefA:"GO:0003824"

pxrefB

Interactor xref B (or Identifier B)

24, 2

pxrefB:"GO:0003824"

pxref

Interactor xrefs (A or B or Identifier A or Identifier B)

23, 24, 1, 2

pxref:"catalytic activity"

xref

Interaction xrefs (or Interaction identifiers)

25, 14

xref:nuclear pore

annot

Interaction annotations and tags

28

annot:"internally curated"

udate

Update date

32

udate:[20100101 TO 20120101]

negative

Negative interaction boolean

36

negative:true

complex

Complex expansion

16

complex:"spoke expanded" or complex:"MI:1060"

ftypeA

Feature type of participant A

37

ftypeA:"sufficient to bind"

ftypeB

Feature type of participant B

38

ftypeB:mutation

ftype

Feature type of participant A or B

37, 38

ftype:"binding site"

pmethodA

Participant identification method A

41

pmethodA:"western blot"

pmethodB

Participant identification method B

42

pmethodB:"sequence tag identification"

pmethod

Participant identification methods (A or B)

41, 42

pmethod:immunostaining

stc

Stoichiometry (A or B). Only true or false, just to be able to filter interaction having stoichiometry available

39, 40

stc:true

param

Interaction parameters. Only true or false, just to be able to filter interaction having parameters available